Loading LATTICE in Protégé

How to open any LATTICE ontology in Protégé with its import closure resolved from the checkout, and how to confirm the generated catalogs are what resolved it (ADR-A88). This is the manual step in the AOR-4 Validation Pack.

Why a successful load is evidence

LATTICE imports its layers by version IRI, for example https://www.nebularis.org/neuro-semantic/lattice/foundation/0.3.0. None of these IRIs is served on the web. If Protégé loads a layer’s imports, it found them through a catalog. Protégé reads the catalog-v001.xml beside the file it opens. In every spec/ and vocab/ directory that file is a stub with one nextCatalog entry pointing at ontology/catalog-v001.xml, which maps every LATTICE IRI to a file.

Before you start

• Protégé 5.6 (desktop).

• From the repository root, confirm the catalogs are current:

  mise run check:ontology-catalog
  

• Note the output of git status --short ontology, so you can tell afterwards whether Protégé rewrote anything.

Test 1: a layer with a deep import closure

1. Start Protégé. Choose File → Open… and select ontology/behaviour/spec/behaviour.ttl. Open the file, not a recent-files entry or a URL.
2. Expected: the ontology opens with no “missing imports” or “could not load import” dialog. Loading may take a few seconds while Protégé fetches the external imports (PROV-O and SKOS) from the W3C, which the root catalog maps to their published locations.
3. Open the ontology selector (the drop-down naming the active ontology at the top of the window). Expected: it lists Behaviour together with Foundation, Vocabulary, Quantification, Party, Eligibility and Instrument, plus PROV-O and SKOS.
4. Select Foundation in that selector. The window title shows the active ontology’s IRI and its physical location. Expected: a file path ending in ontology/foundation/spec/foundation.ttl in your checkout.
5. In the Entities tab, find fnd:DerivedArtefact. Expected: present, with superclass prov:Entity. That confirms both the local Foundation file and the external PROV-O loaded.

Test 2: remove the root catalog (negative control)

1. Close the ontology in Protégé without saving.

2. Temporarily rename the root catalog:

   mv ontology/catalog-v001.xml ontology/catalog-v001.xml.off
   

3. Open ontology/behaviour/spec/behaviour.ttl again.
4. Expected: Protégé reports the LATTICE imports it cannot load. This shows that Test 1 depended on the stub chaining to the root catalog.

5. Cancel or skip the missing imports, close without saving, and restore the catalog:

   mv ontology/catalog-v001.xml.off ontology/catalog-v001.xml
   

Test 3: a MORK-family document

1. Open ontology/mork/spec/Executable.ttl.
2. Expected: no missing-import dialog. It imports MORK by its unversioned ontology IRI, and MORK imports Foundation by version IRI, so this exercises both kinds of catalog entry.

Afterwards

1. Quit Protégé without saving any ontology.

2. Run:

   git status --short ontology
   

   Expected: the same output as before you started. Protégé can add entries to a catalog when you use its import wizard or save. If a catalog-v001.xml changed, restore the generated version:

   mise run build:ontology-catalog
   

3. Confirm:

   mise run check:ontology-catalog
   

Reporting

Record the result in the AOR-4 Validation Pack sign-off (docs/developer/validation/LOG.md).

If Test 1 shows missing LATTICE imports, Protégé did not follow the stub’s relative nextCatalog. That is the open question in ADR-A88. Report which imports were missing. The fallback is to generate full catalogs in every directory instead of stubs.